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talagayev merged 3 commits into from
Feb 1, 2026
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Small addition to ReadMe.md #182

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Update README.md
talagayev Feb 1, 2026
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talagayev Feb 1, 2026
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talagayev Feb 1, 2026
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10 changes: 6 additions & 4 deletions README.md
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Expand Up @@ -13,13 +13,13 @@ OpenMMDL @ Molecular Design Lab
| **Style** | [![Code style: black][badge_black]][url_black]|
| **Linting** | [![ruff][badge_ruff]][url_ruff]|
| **Dependencies** | [![rdkit][badge_rdkit]][url_rdkit] [![mdanalysis][badge_mda]][url_mda]|
| **License** | [![License: GPL v2][badge_license]][url_license]|
| **License** | [![License: MIT][badge_license]][url_license]|


Interface for easy setup and analysis of molecular dynamic (MD) simulations of
protein-ligand complexes with **OpenMM**

http://openmmdl.readthedocs.io/
📖 Documentation: http://openmmdl.readthedocs.io/

## Installation via conda-forge

Expand Down Expand Up @@ -65,7 +65,7 @@ be easily installed on a separate environment using conda (we recommend
using miniconda):

cd OpenMMDL
conda create -n openmmdl -c conda-forge --file requirements.txt
conda env create -f environment.yml -n openmmdl

After installation, activate the conda environment:

Expand Down Expand Up @@ -173,6 +173,8 @@ Start the analysis with the following Inputs:

--figure = File type for the figures, default is png. Can be changed to all file types supported by matplotlib.

--interaction_package = The package used to calculate protein-ligand interactions. The default is PLIP. Alternatively, ProLIF can be used.

#### Command line example with default values

openmmdl analysis -t {path/to/topology} -d {path/to/trajectory} -n {Ligand_name}
Expand Down Expand Up @@ -239,7 +241,7 @@ This Project is based on the
[url_latest_release]: https://github.com/wolberlab/openmmdl/releases
[url_ci_cd]: https://github.com/wolberlab/OpenMMDL/actions/workflows/CI-CD.yml
[url_codeql]: https://github.com/wolberlab/OpenMMDL/actions/workflows/codeql.yml
[url_docs]: https://github.com/wolberlab/OpenMMDL/actions/workflows/codeql.yml
[url_docs]: https://openmmdl.readthedocs.io/en/stable/
[url_codecov]: https://github.com/wolberlab/OpenMMDL/actions/workflows/codeql.yml
[url_conda_forge]: https://anaconda.org/conda-forge/openmmdl
[url_rdkit]: https://www.rdkit.org/
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